Document
29/07/10 François Fages - Ecoles Jeunes Chercheurs - Porquerolles 1
Computational Methods for
Systems Biology and Synthetic
Biology
François Fages,
Constraint Programming Group,
INRIA Rocquencourt
mailto:Francois.Fages@inria.fr
http://contraintes.inria.fr/
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Overview of the Lectures
1. Introduction
"Transposing concepts from programming to the analysis of living processes
2. Rule-based Modeling in Biocham
"Macromolecules, compartments and elementary processes in the cell
"Boolean, Differential and Stochastic interpretations of reaction rule models
"Cell signaling, Gene expression, Retrovirus, Cell cycle
3. Temporal Logic constraints in Biocham
"Qualitative properties in propositional Computation Tree Logic CTL
"Quantitative properties in quantifier-free Linear Time Logic LTL(R)
"Parameter optimization and robustness w.r.t. temporal logic properties
"Conclusion
"Killer lecture: abstract interpretation in Biocham
29/07/10 François Fages - Ecoles Jeunes Chercheurs - Porquerolles 3
Cell Cycle Control by Cyclins: G1SG2M
G1: CdK4-CycD S: Cdk2-CycA G2,M: Cdk1-CycA
Cdk6-CycD Cdk1-CycB (MPF)
Cdk2-CycE
Sir Paul Nurse
Nobel prize 2001
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29/07/10 François Fages - Ecoles Jeunes Chercheurs - Porquerolles 5
Mammalian Cell Cycle Control Map [Kohn 99]
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